Contacts of the helix formed by residues 62 - 74 (chain A) in PDB entry 2VR1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ILE 4.0 3.0 + - - -
57A VAL 3.8 8.5 + - - +
58A LYS* 3.2 47.6 + - - +
59A SER 3.0 15.5 + - - +
60A TYR 3.5 0.2 - - - -
61A LEU* 1.3 73.9 - - - +
63A ILE* 1.3 62.8 + - - +
64A PRO* 3.3 20.1 - - - +
65A ALA* 3.2 24.9 + - + +
66A ILE* 3.1 25.0 + - - +
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU 2.9 16.8 + - - +
62A ASN* 1.3 70.8 - - - +
64A PRO* 1.3 76.6 - - + +
65A ALA 3.2 0.2 + - - -
66A ILE* 3.2 2.8 + - - +
67A ILE* 3.1 36.4 + - + +
85A LEU* 4.0 12.1 - - + -
88A ASN* 4.8 6.7 - - - +
90A ASN* 5.0 2.7 - - + -
91A PHE* 3.6 53.8 - - + +
94A GLN* 3.6 31.0 - - + +
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Residues in contact with PRO 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASN* 3.3 12.8 - - - +
63A ILE* 1.3 96.7 - - + +
65A ALA* 1.3 57.2 + - - +
67A ILE* 3.9 5.5 - - + +
68A SER* 3.0 31.7 + - - -
94A GLN* 6.1 0.4 - - - +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ILE* 3.6 32.3 - - + +
62A ASN* 3.2 35.1 + - + +
63A ILE 3.2 1.0 - - - -
64A PRO* 1.3 78.4 - - - +
66A ILE* 1.3 62.9 + - - +
68A SER* 3.5 6.2 + - - -
69A ALA* 3.2 22.7 + - - +
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 4.4 8.0 - - + +
8A ALA* 4.1 24.2 - - + -
31A VAL* 4.6 7.0 - - + -
51A ILE* 3.8 19.7 - - + -
59A SER 3.9 7.2 - - - +
60A TYR* 3.7 16.2 - - + +
62A ASN 3.1 18.6 + - - +
63A ILE 3.2 3.8 + - - +
65A ALA* 1.3 76.5 - - - +
67A ILE* 1.3 61.9 + - - +
69A ALA* 3.5 8.6 + - - +
70A ALA* 3.3 19.4 + - - +
78A ILE* 4.0 21.3 - - + +
85A LEU* 3.6 28.0 - - + -
91A PHE* 4.1 10.8 - - + -
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Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE* 3.1 34.5 + - + +
64A PRO* 4.0 5.6 - - + +
66A ILE* 1.3 73.9 - - - +
68A SER* 1.3 60.6 + - - +
70A ALA* 3.3 8.2 + - - +
71A GLU* 2.9 45.2 + - - +
78A ILE* 4.9 4.3 - - + -
91A PHE* 4.5 9.4 - - + -
94A GLN* 3.9 26.2 - - + +
95A VAL* 4.2 11.0 - - + +
98A SER* 3.9 28.9 - - - +
100A PHE* 4.2 6.5 - - + -
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A PRO 3.0 19.1 + - - -
65A ALA* 3.6 7.2 - - - -
67A ILE* 1.3 73.4 - - - +
69A ALA* 1.3 56.1 + - - -
71A GLU* 3.0 12.4 + - - +
72A ILE* 2.7 39.0 + - - +
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 4.6 2.7 - - + -
29A VAL* 5.1 0.4 - - + -
31A VAL* 3.5 31.6 - - + -
49A VAL* 4.1 20.0 - - + -
51A ILE* 4.5 0.7 - - + -
65A ALA 3.2 11.1 + - - +
66A ILE 3.6 8.3 - - - +
67A ILE 3.3 0.2 - - - -
68A SER* 1.3 78.6 - - - +
70A ALA* 1.3 56.8 + - - +
72A ILE* 3.4 9.4 - - - +
73A THR* 2.6 39.7 + - - +
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.8 18.5 - - + +
66A ILE 3.3 9.3 + - - +
67A ILE 3.3 9.9 - - - +
69A ALA* 1.3 79.4 - - - +
71A GLU* 1.3 62.3 + - - +
73A THR* 3.8 4.3 - - - -
74A GLY* 3.2 4.9 + - - -
75A ALA* 3.1 29.5 + - + +
78A ILE* 4.2 11.4 - - + -
100A PHE* 3.7 29.3 - - + -
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ILE* 2.9 33.3 + - - +
68A SER* 3.0 11.7 + - - +
70A ALA* 1.3 77.3 - - - +
72A ILE* 1.3 61.2 + - - +
74A GLY* 3.5 9.1 + - - -
98A SER* 4.7 6.2 - - - +
100A PHE* 3.5 22.6 - - + -
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL* 4.8 9.9 - - + -
68A SER* 2.7 18.7 + - - +
69A ALA* 3.4 16.4 - - - +
71A GLU* 1.3 73.8 - - - +
73A THR* 1.3 69.8 + - + +
74A GLY 3.6 0.5 + - - -
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Residues in contact with THR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LYS* 2.7 30.7 + - - +
29A VAL* 3.7 19.9 - - + +
47A GLU* 3.7 25.8 - - + +
49A VAL* 3.7 26.5 - - + -
69A ALA 2.6 26.5 + - - +
70A ALA* 3.2 6.2 + - - -
72A ILE* 1.3 80.2 - - + +
74A GLY* 1.3 57.0 + - - +
75A ALA* 3.6 12.1 + - - +
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Residues in contact with GLY 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ASP* 4.9 3.3 - - - +
4A LYS* 4.1 8.0 - - - +
70A ALA 3.2 6.0 + - - -
71A GLU* 3.5 7.1 + - - -
72A ILE 3.3 3.8 - - - -
73A THR* 1.3 79.0 - - - +
75A ALA* 1.3 65.6 + - - +
76A VAL* 3.9 8.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il